Genome-wide association study for yield-related traits in Sichuan wheat germplasm under stripe rust stress

Authors: YE, XUELING - Sichuan Agricultural University; LI, JIAN - Sichuan Agricultural University; CHENG, YUKUN - Sichuan Agricultural University; YAO, FANGJIE - Sichuan Agricultural University; LONG, LI - Sichuan Agricultural University; YU, CAN - Sichuan Agricultural University; WANG, YUQI - Sichuan Agricultural University; WU, YU - Sichuan Agricultural University; LI, JING - Sichuan Agricultural University; WANG, JIRUI - Sichuan Agricultural University; JIANG, QIANTAO - Sichuan Agricultural University; LI, WEI - Sichuan Agricultural University; MA, JIAN - Sichuan Agricultural University; WEI, YUMING - Sichuan Agricultural University; Chen, Xianming; ZHENG, YOULIANG - Sichuan Agricultural University; CHEN, GUOYUE - Sichuan Agricultural University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2019
Publication Date: 8/8/2019
Citation: Ye, X., Li, J., Cheng, Y., Yao, F., Long, L., Yu, C., Wang, Y., Wu, Y., Li, J., Wang, J., Jiang, Q., Li, W., Ma, J., Wei, Y., Chen, X., Zheng, Y., Chen, G. 2019. Genome-wide association study for yield-related traits in Sichuan wheat germplasm under stripe rust stress. BMC Genomics. BMC Genomics 20:640. https://doi.org/10.1186/s12864-019-6005-6.
DOI: https://doi.org/10.1186/s12864-019-6005-6

Interpretive Summary: As one of the most important food crops in the world, increasing wheat yield is an urgent task for global food security under the continuous threat of stripe rust in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44059 polymorphic markers from the 55K single nucleotide polymorphism (SNP) chip. A total of 18 loci were found to be highly associating to yield-related traits, including 7 for spike length (SL), 5 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 4 for TKW and KWPS, in at least two test environments under stripe rust stress conditions. The SL association loci were located on chromosome 1A, 2A, 2D, 4A and 5A, and the TKW and KWPS association loci were mapped on chromosome 1B, 2A and 4A, respectively. In particular, the loci at chromosome 1A associated with SL were identified in all three environments, and the loci explained up to 20% phenotypic variation of KWPS. Three of the 18 loci are potentially new. The SNP markers for the favourable alleles may be used in marker-assisted selection in wheat breeding programs.

Technical Abstract: As one of the most important food crops in the world, increasing wheat (Triticum aestivum) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44059 polymorphic markers from the 55K single nucleotide polymorphism (SNP) chip. A total of 18 loci were found to be highly associating to yield-related traits, including 7 for spike length (SL), 5 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 4 for TKW and KWPS, in at least two test environments under stripe rust stress conditions. The SL association loci were located on chromosome 1A, 2A, 2D, 4A and 5A, and the TKW and KWPS association loci were mapped on chromosome 1B, 2A and 4A, respectively. In particular, the loci at chromosome 1A associated with SL were identified in all three environments, and the loci explained up to 20% phenotypic variation of KWPS. Three of the 18 loci are potentially new. The SNP markers for the favourable alleles may be used in marker-assisted selection in wheat breeding programs.